| Calling Sequence
| ProbAncestor(ps1,ps2,d1,d2)
ProbAncestor(ps1,ps2,d1,d2,lnM,freq)
|
| Parameters
| | Name | Type | Description |
|
| ps1, ps2
| ProbSeq | Probabilistic sequences |
| d1, d2
| numeric | Distances to the common ancestor |
| lnM
| matrix(numeric) | (optional) log. of a 1-PAM matrix |
| freq
| array(numeric) | (optional) character frequencies |
|
| Return Type
| ProbSeq |
| Globals
| LogLikelihoods, |
| Synopsis
| Given two probabilistic sequences and the distances to their
common ancestor, this function computes the probabilistic ancestral sequence (PAS). The
logarithm of a 1-PAM matrix is needed to compute the mutation matrices for the
two distances. The mutation matrix NewlogPAM1 is the default value and can be used
for amino acid sequences. For codon sequences CodonLogPAM1 is recommended. The ancestral
probabilities depend on the natural frequencies of the characters. By default, the
amino acid frequencies AF are used. The global variable LogLikelihoods will be assigned
to an array containing the ln of the likelihoods at each position. |
| References
| GM Cannarozzi, A Schneider and GH Gonnet (2007): Probabilistic Ancestral Sequences Based on the Markovian Model of Evolution - Algorithms and Applications, in: D Liberless (editor): Ancestral Sequence Reconstruction, Oxford University Press. |
| Examples
| > ps1 := ProbSeq('AARV',IntToA):
> ps2 := ProbSeq('AVVV',IntToA):
> pas := ProbAncestor(ps1,ps2,10,10):
> print(pas);;
pos Most probable chars
1 A 1.00 S 0.00 V 0.00 G 0.00 T 0.00
2 A 0.56 V 0.43 L 0.00 T 0.00 I 0.00
3 V 0.56 R 0.34 A 0.02 L 0.02 K 0.02
4 V 1.00 I 0.00 L 0.00 A 0.00 T 0.00
|
| See also
| CreateCodonMatrices, CreateDayMatrices, PASfromMSA, PASfromTree, ProbSeq, PSDynProg |